Red Lists are used to assess the extinction risk of species. Regional IUCN criteria were applied to categorise 42 indigenous freshwater fish species in Flanders into Red List categories. As such, three species are assessed as Regionally Extinct, eight as Critically Endangered, two as Endangered and eight as Vulnerable. A further five species are considered Near Threatened, 15 species as Least Concern and one species is Data Deficient. Five species disappeared from the Regionally Extinct category compared with the previous Red List (1988) as a consequence of improved water quality of estuaries and reintroduction programmes. In total, 62% of the freshwater fish species in Flanders was considered extinct or threatened. This is higher than neighbouring regions and Europe as a whole (44%). This new Red List of freshwater fishes in Flanders can be used to inform conservation actions.